We have undertaken a program that is aimed at determining, on a molecular level, those genetic alterations in primary breast tumor DNA that have a statistically significant association with the patients history, characteristics of the tumor, and the patients prognosis. The most frequent type of mutation is loss of heterozygosity (LOH) at specific regions of the cellular genome in tumor DNA. Approximately 20 such regions have been identified in breast tumor DNAs. One of these is located on chromosome 17q12-q21. Using polymorphic markers from this region we were able to show that the 120-150 kb interval between D17S846 and D17S746 represents the smallest common region which is deleted. To identify the target gene(s) for LOH we are currently determining the nucleotide sequence of two overlapping P1 phage clones which span this region. We have found two candidate target genes. One of these is the gene (PLAK) encoding plakoglobin, a component of the cadherin-catenin complex which anchors actin filaments at adherens junctions of epithelial cells. The gene is composed of 13 exons which span 13 kb at the non overlapping end of one of the P1 phage clones. No mutations were found in nine breast tumor cell lines by SSCP analysis (SK-BR-3, ZR-75- 1, MDA-MB-231, T-47D, BT-20, MDA-MB-468, HS 578T, MCF-7, and BT-474). Similarly, no mutations were detected in genomic DNA or cDNA fromeleven breast tumors known to have LOH in the region containing PLAK. A second candidate gene has been identified in the region of overlap between the two P1 phage clones. It is a member of a family of genes encoding immunophilins which are highly conserved intracellular receptors. Currently we are determining the organization of this gene and whether it is mutated in breast tumors having LOH on 17q12-q21.